Required Packages and functions

# libraries
library(sas7bdat)
library(sva)
library(reshape)
library(ggplot2)
library(gridExtra)
library(knitr)
library(dplyr)
library(kableExtra)
library(tidyverse)
library(minfi)
library(stringr)
library(limma)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(minfi)
library(DMRcate)
library(UpSetR)
library(reshape)
library(corrplot)
library(factoextra)
library(ENmix)
library(missMethyl)

# loading annotation
anno = getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
anno = data.frame(anno)

# loading functions
setwd('/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local')
source('EWAS functions.R')

Load DNAm and pheno data

load("/Users/annebozack/Box/NIEHS-R01 ONES/Methylation Data/CordBlood_ComBat_Betas_Mvals_filteredProbes_metalAnalysis.RData")

dim(pDatcordMetal)
# 361 164

dim(ComBat.Mvalues.Metals)
# 394460    361

rownames(pDatcordMetal) = pDatcordMetal$samplename

EWAS

As

DMP_As_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal, var = 'As_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/As')

# Unadjusted, N =  361 
# Unadjusted, p<0.05:  11440 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  361 
# Adjusted, p<0.05:  19530 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.065045 
 
# Number of DMRs identified:   1 

# rm(DMP_As_cord); gc()

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals)
y = pDatcordMetal$As_log2
X = model.matrix(~ female_d + race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.1888243

TestCDFs2(Z = Z, y = y, X = X)
# 0.4438389

# rm(DMP_As_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
12 9217389 9217859 0 470 0 0 9

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/As/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/As/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/As/As_log2_manhattan_DMP_adj.png")

As, female

pDatcordMetal_F = pDatcordMetal[pDatcordMetal$female_d == 1,]
pDatcordMetal_F$race_child2 = as.factor(as.numeric(pDatcordMetal_F$race_child2))

DMP_As_F_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_F, var = 'As_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/As_F')

# Unadjusted, N =  169 
# Unadjusted, p<0.05:  17949 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  169 
# Adjusted, p<0.05:  16668 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9807579 

# Number of DMRs identified:   2 

# Global DNAm
ComBat.Betas.Metals_F = ComBat.Betas.Metals[,colnames(ComBat.Betas.Metals) %in% rownames(pDatcordMetal_F)]
ComBat.Betas.Metals_F = ComBat.Betas.Metals_F[,match(rownames(pDatcordMetal_F), colnames(ComBat.Betas.Metals_F))]

Z = as.matrix(ComBat.Betas.Metals_F)
y = pDatcordMetal_F$As_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_F)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.2559703

TestCDFs2(Z = Z, y = y, X = X)
# 0.6246159

# rm(DMP_As_F_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
3 186490655 186490915 0 260 0 1.8e-06 5
11 34460106 34460386 0 280 0 4.7e-06 7

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/As_F/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/As_F/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/As_F/As_log2_manhattan_DMP_adj.png")

As, male

pDatcordMetal_M = pDatcordMetal[pDatcordMetal$female_d == 0,]
pDatcordMetal_M$race_child2 = as.factor(as.numeric(pDatcordMetal_M$race_child2))

DMP_As_M_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_M, var = 'As_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/As_M')

# Unadjusted, N =  192 
# Unadjusted, p<0.05:  12218 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  192 
# Adjusted, p<0.05:  17743 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.011027 
 
# Number of DMRs identified:   6 

# Global DNAm
ComBat.Betas.Metals_M = ComBat.Betas.Metals[,colnames(ComBat.Betas.Metals) %in% rownames(pDatcordMetal_M)]
ComBat.Betas.Metals_M = ComBat.Betas.Metals_M[,match(rownames(pDatcordMetal_M), colnames(ComBat.Betas.Metals_M))]

Z = as.matrix(ComBat.Betas.Metals_M)
y = pDatcordMetal_M$As_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_M)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.5073422

TestCDFs2(Z = Z, y = y, X = X)
# 0.4807815

# rm(DMP_As_M_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
12 9217389 9217859 0.0000000 470 0.0000000 0.0000000 9
20 3051953 3052345 0.0000000 392 0.0000000 0.0000001 9
11 18433499 18433683 0.0000000 184 0.0000001 0.0000770 4
11 2890628 2890670 0.0000178 42 0.0000214 0.1539887 6
11 1036676 1036766 0.0000179 90 0.0000214 0.0753032 3
6 32063990 32064032 0.0060759 42 0.0060759 1.0000000 2

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/As_M/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/As_M/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/As_M/As_log2_manhattan_DMP_adj.png")

Ba

DMP_Ba_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal, var = 'Ba_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Ba')

# Unadjusted, N =  361 
# Unadjusted, p<0.05:  21408 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  361 
# Adjusted, p<0.05:  18967 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.006289 
 
# Number of identified DMR:  0

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals)
y = pDatcordMetal$Ba_log2
X = model.matrix(~ female_d + race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 1

TestCDFs2(Z = Z, y = y, X = X)
# 0.9650461

# rm(DMP_Ba_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
NA NA NA NA NA NA NA NA
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Ba/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Ba/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Ba/Ba_log2_manhattan_DMP_adj.png")

Ba, female

DMP_Ba_F_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_F, var = 'Ba_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Ba_F')

# Unadjusted, N =  169 
# Unadjusted, p<0.05:  16994 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  169 
# Adjusted, p<0.05:  13428 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.7990795 

# Number of DMRs identified:   2 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_F)
y = pDatcordMetal_F$Ba_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_F)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.864574

TestCDFs2(Z = Z, y = y, X = X)
# 0.9088558

# rm(DMP_Ba_F_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
10 135051255 135051581 0 326 0 2e-06 7
8 144635259 144635610 0 351 0 5e-06 9
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Ba_F/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Ba_F/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Ba_F/Ba_log2_manhattan_DMP_adj.png")

Ba, male

DMP_Ba_M_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_M, var = 'Ba_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Ba_M')

# Unadjusted, N =  192 
# Unadjusted, p<0.05:  16173 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  192 
# Adjusted, p<0.05:  14282 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.865515 
 
# Number of DMRs identified:   2 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_M)
y = pDatcordMetal_M$Ba_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_M)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.6927273

TestCDFs2(Z = Z, y = y, X = X)
# 0.8277251

# rm(DMP_Ba_M_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
4 169239618 169240010 0 392 0 0e+00 7
10 135278716 135279147 0 431 0 2e-07 5
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Ba_M/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Ba_M/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Ba_M/Ba_log2_manhattan_DMP_adj.png")

Cd

DMP_Cd_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal, var = 'Cd_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cd')

# Unadjusted, N =  361 
# Unadjusted, p<0.05:  13284 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  361 
# Adjusted, p<0.05:  16155 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9008795 

# Number of DMRs identified:   5 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals)
y = pDatcordMetal$Cd_log2
X = model.matrix(~ female_d + race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 1

TestCDFs2(Z = Z, y = y, X = X)
# 0.9348243

# rm(DMP_Cd_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
3 156323951 156324118 0.0000000 167 0.0000000 0.0000030 3
13 110319561 110319607 0.0000000 46 0.0000000 0.0000233 3
17 46685291 46685448 0.0000000 157 0.0000000 0.0000207 5
2 200468625 200468832 0.0000001 207 0.0000001 0.0001106 3
6 30039141 30039175 0.0095070 34 0.0095070 1.0000000 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cd/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cd/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cd/Cd_log2_manhattan_DMP_adj.png")

Cd, female

DMP_Cd_F_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_F, var = 'Cd_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cd_F')

# Unadjusted, N =  169 
# Unadjusted, p<0.05:  19177 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  169 
# Adjusted, p<0.05:  18135 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9732893 
 
# Number of DMRs identified:   2 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_F)
y = pDatcordMetal_F$Cd_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_F)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.6678424

TestCDFs2(Z = Z, y = y, X = X)
# 0.7811745

# rm(DMP_Cd_F_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
7 27225810 27225897 2.0e-07 87 4.0e-07 0.0009656 4
2 200468625 200468728 4.5e-06 103 4.5e-06 0.0171663 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cd_F/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cd_F/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cd_F/Cd_log2_manhattan_DMP_adj.png")

Cd, male

DMP_Cd_M_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_M, var = 'Cd_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cd_M')

# Unadjusted, N =  192 
# Unadjusted, p<0.05:  8842 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  192 
# Adjusted, p<0.05:  15768 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9683207 
 
# Number of DMRs identified:   1

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_M)
y = pDatcordMetal_M$Cd_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_M)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 1

TestCDFs2(Z = Z, y = y, X = X)
# 0.4173395
 
# rm(DMP_Cd_M_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
19 37742738 37742956 0 218 0 1e-07 4
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cd_M/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cd_M/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cd_M/Cd_log2_manhattan_DMP_adj.png")

Cr

DMP_Cr_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal, var = 'Cr_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cr')

# Unadjusted, N =  361 
# Unadjusted, p<0.05:  19469 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  361 
# Adjusted, p<0.05:  19356 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9710716 

# Number of DMRs identified:   5 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals)
y = pDatcordMetal$Cr_log2
X = model.matrix(~ female_d + race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.8160506

TestCDFs2(Z = Z, y = y, X = X)
# 0.8524831

# rm(DMP_Cr_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
8 13373032 13373141 0.0e+00 109 0.0e+00 0.0000063 3
6 33245700 33246008 0.0e+00 308 0.0e+00 0.0000023 13
10 114713023 114713187 0.0e+00 164 0.0e+00 0.0000259 3
17 46681110 46681401 0.0e+00 291 1.0e-07 0.0000623 6
17 46641862 46642011 8.8e-05 149 8.8e-05 0.2079115 2

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cr/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cr/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cr/Cr_log2_manhattan_DMP_adj.png")

Cr, female

DMP_Cr_F_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_F, var = 'Cr_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cr_F')

# Unadjusted, N =  169 
# Unadjusted, p<0.05:  15600 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  169 
# Adjusted, p<0.05:  13645 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8363976 
 
# Number of DMRs identified:   2 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_F)
y = pDatcordMetal_F$Cr_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_F)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 1

TestCDFs2(Z = Z, y = y, X = X)
# 0.9279794

# rm(DMP_Cr_F_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
8 13373032 13373141 0e+00 109 0e+00 0.0000145 3
6 31148369 31148666 1e-07 297 1e-07 0.0001264 12
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cr_F/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cr_F/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cr_F/Cr_log2_manhattan_DMP_adj.png")

Cr, male

DMP_Cr_M_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_M, var = 'Cr_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cr_M')

# Unadjusted, N =  192 
# Unadjusted, p<0.05:  13268 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  192 
# Adjusted, p<0.05:  15910 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.909677 

# Number of identified DMR:  0

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_M)
y = pDatcordMetal_M$Cr_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_M)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.5576744

TestCDFs2(Z = Z, y = y, X = X)
# 0.7528378

rm(DMP_Cr_M_cord); gc()
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cr_M/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cr_M/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cr_M/Cr_log2_manhattan_DMP_adj.png")

Cs

DMP_Cs_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal, var = 'Cs_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cs')

# Unadjusted, N =  361 
# Unadjusted, p<0.05:  28868 
# Unadjusted, FDR<0.05:  5 
# Unadjusted, pBonf<0.05:  3 
 
# Adjusted, N =  361 
# Adjusted, p<0.05:  19239 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.018459 

# Number of DMRs identified:   18 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals)
y = pDatcordMetal$Cs_log2
X = model.matrix(~ female_d + race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.5068162

TestCDFs2(Z = Z, y = y, X = X)
# 0.5042182

# rm(DMP_Cs_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
4 174421376 174422626 0.0000000 1250 0.0000000 0.0000000 7
6 33280051 33280478 0.0000000 427 0.0000000 0.0000000 14
6 28601268 28601519 0.0000000 251 0.0000000 0.0000001 11
6 32847440 32847845 0.0000000 405 0.0000000 0.0000003 17
6 30881315 30881842 0.0000000 527 0.0000000 0.0000002 21
17 17603530 17603837 0.0000000 307 0.0000000 0.0000008 4
20 57427411 57427762 0.0000000 351 0.0000000 0.0000016 15
1 75590911 75591029 0.0000000 118 0.0000000 0.0000167 3
12 44152508 44152940 0.0000000 432 0.0000000 0.0000091 11
12 1025528 1025755 0.0000001 227 0.0000001 0.0000898 3
12 54763210 54763433 0.0000001 223 0.0000001 0.0000934 3
19 10736005 10736117 0.0000001 112 0.0000001 0.0002107 5
3 141087186 141087363 0.0000001 177 0.0000001 0.0001661 5
8 43131259 43131656 0.0000001 397 0.0000001 0.0000851 5
15 69325270 69325560 0.0000001 290 0.0000001 0.0001177 5
5 78985424 78985592 0.0000002 168 0.0000002 0.0003553 9
17 46388389 46388465 0.0000002 76 0.0000003 0.0012942 3
6 31651019 31651029 0.0061778 10 0.0061778 1.0000000 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cs/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cs/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cs/Cs_log2_manhattan_DMP_adj.png")

Cs, female

DMP_Cs_F_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_F, var = 'Cs_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cs_F')

# Unadjusted, N =  169 
# Unadjusted, p<0.05:  14228 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  169 
# Adjusted, p<0.05:  11077 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.7878935 
 
# Number of DMRs identified:   4 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_F)
y = pDatcordMetal_F$Cs_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_F)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.683642

TestCDFs2(Z = Z, y = y, X = X)
# 0.9583828

# rm(DMP_Cs_F_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
12 44152508 44152940 0.00e+00 432 0.00e+00 0.0000000 11
6 117923794 117924070 0.00e+00 276 0.00e+00 0.0000220 8
1 26233331 26233623 0.00e+00 292 1.00e-07 0.0000511 10
6 32847761 32847830 1.61e-05 69 1.61e-05 0.0879654 5
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cs_F/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cs_F/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cs_F/Cs_log2_manhattan_DMP_adj.png")

Cs, male

DMP_Cs_M_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_M, var = 'Cs_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cs_M')

# Unadjusted, N =  192 
# Unadjusted, p<0.05:  23725 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  192 
# Adjusted, p<0.05:  21075 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.092447 

# Number of DMRs identified:   14 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_M)
y = pDatcordMetal_M$Cs_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_M)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.9380089

TestCDFs2(Z = Z, y = y, X = X)
# 0.5680556

# rm(DMP_Cs_M_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
6 31650734 31651362 0e+00 628 0e+00 0.0000000 21
8 43131259 43132507 0e+00 1248 0e+00 0.0000000 8
15 69325270 69325560 0e+00 290 0e+00 0.0000000 5
17 17603530 17604146 0e+00 616 0e+00 0.0000000 5
12 108634146 108634275 0e+00 129 0e+00 0.0000017 3
6 28601268 28601519 0e+00 251 0e+00 0.0000024 11
3 141087186 141087363 0e+00 177 0e+00 0.0000098 5
10 134150488 134150760 0e+00 272 1e-07 0.0000454 7
6 30881463 30881766 1e-07 303 1e-07 0.0001063 15
19 51774376 51774666 1e-07 290 1e-07 0.0001355 4
14 21148813 21148957 1e-07 144 1e-07 0.0003044 2
6 28446839 28447115 1e-07 276 2e-07 0.0002057 4
4 187422004 187422119 2e-07 115 2e-07 0.0006142 5
13 23309929 23310203 4e-07 274 4e-07 0.0005223 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cs_M/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cs_M/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cs_M/Cs_log2_manhattan_DMP_adj.png")

Cu

DMP_Cu_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal, var = 'Cu_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cu')

# Unadjusted, N =  361 
# Unadjusted, p<0.05:  31830 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  361 
# Adjusted, p<0.05:  57348 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.845378 

# Number of DMRs identified:   4 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals)
y = pDatcordMetal$Cu_log2
X = model.matrix(~ female_d + race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.3984576

TestCDFs2(Z = Z, y = y, X = X)
# 0.05580438

# rm(DMP_Cu_cord); gc()

FDR-significant DMPs

x
NA

DMRs

chr start end p length fdr sidak nprobe
4 174421376 174422626 0.0000000 1250 0.0000000 0.0000000 7
6 33280051 33280478 0.0000000 427 0.0000000 0.0000000 14
6 28601268 28601519 0.0000000 251 0.0000000 0.0000001 11
6 32847440 32847845 0.0000000 405 0.0000000 0.0000003 17
6 30881315 30881842 0.0000000 527 0.0000000 0.0000002 21
17 17603530 17603837 0.0000000 307 0.0000000 0.0000008 4
20 57427411 57427762 0.0000000 351 0.0000000 0.0000016 15
1 75590911 75591029 0.0000000 118 0.0000000 0.0000167 3
12 44152508 44152940 0.0000000 432 0.0000000 0.0000091 11
12 1025528 1025755 0.0000001 227 0.0000001 0.0000898 3
12 54763210 54763433 0.0000001 223 0.0000001 0.0000934 3
19 10736005 10736117 0.0000001 112 0.0000001 0.0002107 5
3 141087186 141087363 0.0000001 177 0.0000001 0.0001661 5
8 43131259 43131656 0.0000001 397 0.0000001 0.0000851 5
15 69325270 69325560 0.0000001 290 0.0000001 0.0001177 5
5 78985424 78985592 0.0000002 168 0.0000002 0.0003553 9
17 46388389 46388465 0.0000002 76 0.0000003 0.0012942 3
6 31651019 31651029 0.0061778 10 0.0061778 1.0000000 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cu/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cu/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cu/Cu_log2_manhattan_DMP_adj.png")

Cu, female

DMP_Cu_F_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_F, var = 'Cu_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cu_F')

# Unadjusted, N =  169 
# Unadjusted, p<0.05:  34435 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  169 
# Adjusted, p<0.05:  17137 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.061581 
 
# Number of DMRs identified:   3 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_F)
y = pDatcordMetal_F$Cu_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_F)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.2253006

TestCDFs2(Z = Z, y = y, X = X)
# 0.2135721

# rm(DMP_Cu_F_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
20 57427442 57427830 0.0000000 388 0.0000000 0.0000017 15
7 1250087 1250182 0.0000576 95 0.0000864 0.2126146 3
11 368637 368712 0.0067564 75 0.0067564 1.0000000 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cu_F/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cu_F/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cu_F/Cu_log2_manhattan_DMP_adj.png")

Cu, male

DMP_Cu_M_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_M, var = 'Cu_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cu_M')

# Unadjusted, N =  192 
# Unadjusted, p<0.05:  10164 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  192 
# Adjusted, p<0.05:  57164 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.911863 
 
# Number of DMRs identified:   6 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_M)
y = pDatcordMetal_M$Cu_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_M)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 1

TestCDFs2(Z = Z, y = y, X = X)
# 0.2307306

# rm(DMP_Cu_M); gc()

FDR-significant DMPs

x
NA

DMRs

chr start end p length fdr sidak nprobe
5 83016999 83017184 0.0000000 185 0.0000000 0.0000001 4
3 46759437 46759698 0.0000000 261 0.0000000 0.0000021 7
1 108023248 108023482 0.0000001 234 0.0000001 0.0001015 5
12 54673866 54674009 0.0000036 143 0.0000053 0.0097873 4
6 32847761 32847830 0.0000643 69 0.0000772 0.3076772 5
7 94953876 94953956 0.0049862 80 0.0049862 1.0000000 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cu_M/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cu_M/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Cu_M/Cu_log2_manhattan_DMP_adj.png")

Hg

DMP_Hg_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal, var = 'Hg_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Hg')

# Unadjusted, N =  358 
# Unadjusted, p<0.05:  38119 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  358 
# Adjusted, p<0.05:  13462 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.7929906 
 
# Number of DMRs identified:   2 

# Global DNAm
pDatcordMetal_Hg = pDatcordMetal[!is.na(pDatcordMetal$Hg_log2),]
dim(pDatcordMetal_Hg)
# 358 164

ComBat.Betas.Metals_Hg = ComBat.Betas.Metals[,colnames(ComBat.Betas.Metals) %in% rownames(pDatcordMetal_Hg)]
ComBat.Betas.Metals_Hg = ComBat.Betas.Metals_Hg[,match(rownames(pDatcordMetal_Hg), colnames(ComBat.Betas.Metals_Hg))]

Z = as.matrix(ComBat.Betas.Metals_Hg)
y = pDatcordMetal_Hg$Hg_log2
X = model.matrix(~ female_d + race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_Hg)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 1

TestCDFs2(Z = Z, y = y, X = X)
# 0.845803

# rm(DMP_Hg_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
8 143859668 143859990 0 322 0 0.00e+00 7
6 30039373 30039548 0 175 0 1.99e-05 12
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Hg/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Hg/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Hg/Hg_log2_manhattan_DMP_adj.png")

Hg, female

DMP_Hg_F_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_F, var = 'Hg_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Hg_F')

# Unadjusted, N =  167 
# Unadjusted, p<0.05:  11528 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  167 
# Adjusted, p<0.05:  10298 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.7271097 
 
# Number of DMRs identified:   1 

# Global DNAm
pDatcordMetal_HgF = pDatcordMetal_Hg[pDatcordMetal_Hg$female_d == 1,]
dim(pDatcordMetal_HgF)
# 167 164

ComBat.Betas.Metals_HgF = ComBat.Betas.Metals[,colnames(ComBat.Betas.Metals) %in% rownames(pDatcordMetal_HgF)]
ComBat.Betas.Metals_HgF = ComBat.Betas.Metals_HgF[,match(rownames(pDatcordMetal_HgF), colnames(ComBat.Betas.Metals_HgF))]

Z = as.matrix(ComBat.Betas.Metals_HgF)
y = pDatcordMetal_HgF$Hg_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_HgF)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 1

TestCDFs2(Z = Z, y = y, X = X)
# 0.9751191

# rm(DMP_Hg_F_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
6 31508105 31508137 3.95e-05 32 3.95e-05 0.3855435 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Hg_F/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Hg_F/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Hg_F/Hg_log2_manhattan_DMP_adj.png")

Hg, male

DMP_Hg_M_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_M, var = 'Hg_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Hg_M')

# Unadjusted, N =  191 
# Unadjusted, p<0.05:  32177 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  191 
# Adjusted, p<0.05:  12873 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8093155 
 
# Number of DMRs identified:   3 

# Global DNAm
pDatcordMetal_HgM = pDatcordMetal_Hg[pDatcordMetal_Hg$female_d == 0,]
dim(pDatcordMetal_HgM)
# 191 164

ComBat.Betas.Metals_HgM = ComBat.Betas.Metals[,colnames(ComBat.Betas.Metals) %in% rownames(pDatcordMetal_HgM)]
ComBat.Betas.Metals_HgM = ComBat.Betas.Metals_HgM[,match(rownames(pDatcordMetal_HgM), colnames(ComBat.Betas.Metals_HgM))]

Z = as.matrix(ComBat.Betas.Metals_HgM)
y = pDatcordMetal_HgM$Hg_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_HgM)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 1

TestCDFs2(Z = Z, y = y, X = X)
# 0.8570357

# rm(DMP_Hg_M_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
8 143859668 143859990 0 322 0 0e+00 7
6 31650785 31651362 0 577 0 2e-07 19
6 30039141 30039548 0 407 0 4e-07 15
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Hg_M/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Hg_M/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Hg_M/Hg_log2_manhattan_DMP_adj.png")

Mg

DMP_Mg_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal, var = 'Mg_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mg')

# Unadjusted, N =  361 
# Unadjusted, p<0.05:  20828 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  361 
# Adjusted, p<0.05:  19876 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.067098 

# Number of DMRs identified:   5 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals)
y = pDatcordMetal$Mg_log2
X = model.matrix(~ female_d + race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.469153

TestCDFs2(Z = Z, y = y, X = X)
# 0.3509856

# rm(DMP_Mg_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
20 57427169 57427973 0.0e+00 804 0.0e+00 0.0000000 24
6 30039174 30039548 0.0e+00 374 0.0e+00 0.0000000 13
6 32063990 32064258 0.0e+00 268 1.0e-07 0.0000461 12
1 2980037 2980163 2.5e-06 126 3.1e-06 0.0077603 2
11 368564 368712 6.6e-06 148 6.6e-06 0.0175234 7
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mg/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mg/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mg/Mg_log2_manhattan_DMP_adj.png")

Mg, female

DMP_Mg_F_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_F, var = 'Mg_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mg_F')

# Unadjusted, N =  169 
# Unadjusted, p<0.05:  21465 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  169 
# Adjusted, p<0.05:  15005 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.860424 
 
# Number of DMRs identified:   5

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_F)
y = pDatcordMetal_F$Mg_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_F)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.4382674

TestCDFs2(Z = Z, y = y, X = X)
# 0.5358737

# rm(DMP_Mg_F_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
17 48912264 48912621 0.00e+00 357 0.00e+00 0.0000000 9
20 57427442 57427762 0.00e+00 320 1.00e-07 0.0000298 13
2 121223739 121224009 1.00e-07 270 1.00e-07 0.0001158 6
14 105944941 105945022 1.60e-06 81 2.00e-06 0.0076408 2
19 45976119 45976195 4.01e-05 76 4.01e-05 0.1879917 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mg_F/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mg_F/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mg_F/Mg_log2_manhattan_DMP_adj.png")

Mg, male

DMP_Mg_M_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_M, var = 'Mg_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mg_M')

# Unadjusted, N =  192 
# Unadjusted, p<0.05:  38543 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  192 
# Adjusted, p<0.05:  40446 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.605054 
 
# Number of DMRs identified:   2 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_M)
y = pDatcordMetal_M$Mg_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_M)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.6190037

TestCDFs2(Z = Z, y = y, X = X)
# 0.3666586

# rm(DMP_Mg_M_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
19 57742111 57742423 0.0000000 312 0.0000000 0.0000000 7
22 22901829 22901880 0.0008779 51 0.0008779 0.9988789 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mg_M/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mg_M/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mg_M/Mg_log2_manhattan_DMP_adj.png")

Mn

DMP_Mn_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal, var = 'Mn_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mn')

# Unadjusted, N =  361 
# Unadjusted, p<0.05:  9732 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  361 
# Adjusted, p<0.05:  10167 
# Adjusted, FDR<0.05:  1 
# Adjusted, pBonf<0.05:  1 
# Adjusted, lambda:  0.7325852 
 
# Number of DMRs identified:   2 

# Pathway analysis

GO_Mn = gometh(sig.cpg = DMP_Mn_cord[[3]]$cpg[DMP_Mn_cord[[3]]$adj.P.Val < 0.05], all.cpg = DMP_Mn_cord[[3]]$cpg, collection = "GO")
table(GO_Mn$P.DE < 0.05)
# FALSE  TRUE 
# 22583    27 
table(GO_Mn$FDR < 0.05)
# FALSE 
# 22610 

KEGG_Mn = gometh(sig.cpg = DMP_Mn_cord[[3]]$cpg[DMP_Mn_cord[[3]]$adj.P.Val < 0.05], all.cpg = DMP_Mn_cord[[3]]$cpg, collection = "KEGG")
table(KEGG_Mn$P.DE < 0.05)
# FALSE 
  # 342 
  
# Global DNAm
Z = as.matrix(ComBat.Betas.Metals)
y = pDatcordMetal$Mn_log2
X = model.matrix(~ female_d + race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 1

TestCDFs2(Z = Z, y = y, X = X)
# 0.9723614

# rm(DMP_Mn_cord); gc()

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg02042823 0.43 (0.31 ,0.55) 5.75 0 9.3e-06 0 chr16 6714429 A2BP1;A2BP1

DMRs

chr start end p length fdr sidak nprobe
6 32063725 32064161 0.0000000 436 0.0000000 0.0000038 13
7 1250125 1250182 0.0017739 57 0.0017739 0.9999954 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mn/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mn/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mn/Mn_log2_manhattan_DMP_adj.png")

Mn, female

DMP_Mn_F_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_F, var = 'Mn_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mn_F')

# Unadjusted, N =  169 
# Unadjusted, p<0.05:  26444 
# Unadjusted, FDR<0.05:  3 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  169 
# Adjusted, p<0.05:  13233 
# Adjusted, FDR<0.05:  9 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8939725 
 
# Number of DMRs identified:   7 

GO_Mn_F = gometh(sig.cpg = DMP_Mn_F_cord[[3]]$cpg[DMP_Mn_F_cord[[3]]$adj.P.Val < 0.05], all.cpg = DMP_Mn_F_cord[[3]]$cpg, collection = "GO")
table(GO_Mn_F$P.DE < 0.05)
# FALSE  TRUE 
# 22481   129 
table(GO_Mn_F$FDR < 0.05)
# FALSE 
# 22610 

KEGG_Mn_F = gometh(sig.cpg = DMP_Mn_F_cord[[3]]$cpg[DMP_Mn_F_cord[[3]]$adj.P.Val < 0.05], all.cpg = DMP_Mn_cord_F[[3]]$cpg, collection = "KEGG")
table(KEGG_Mn_F$P.DE < 0.05)
# FALSE  TRUE 
  # 334     8 
table(KEGG_Mn_F$FDR < 0.05)
# FALSE 
  # 342 
  
write.csv(KEGG_Mn_F, '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mn_F/KEGG.csv')

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_F)
y = pDatcordMetal_F$Mn_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_F)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.3499748

TestCDFs2(Z = Z, y = y, X = X)
# 0.7004179

# rm(DMP_Mn_F_cord); gc()

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg00954161 0.42 (0.27 ,0.57) 5.99 2e-07 0.0341269 0.0801 chr1 3696925 LRRC47
cg01744822 -0.22 (-0.31 ,-0.14) -4.36 9e-07 0.0442988 0.3421 chr16 73100510
cg08904630 0.21 (0.13 ,0.29) 5.33 9e-07 0.0442988 0.3514 chr10 71490427
cg11161853 -0.14 (-0.19 ,-0.08) -5.29 9e-07 0.0442988 0.3738 chr3 67705044 SUCLG2
cg15712310 -0.19 (-0.26 ,-0.12) -1.62 2e-07 0.0341269 0.0717 chr16 73100790
cg19908812 -0.17 (-0.24 ,-0.1) -6.02 9e-07 0.0442988 0.3659 chr4 164253006 NPY1R
cg22799518 0.52 (0.33 ,0.71) 6.34 3e-07 0.0341269 0.1365 chr12 56988862 RBMS2
cg23903787 0.34 (0.22 ,0.47) 3.02 3e-07 0.0341269 0.1141 chr4 3527371 LRPAP1
cg26462130 0.39 (0.24 ,0.53) 6.11 1e-06 0.0442988 0.3987 chr7 2052961 MAD1L1;MAD1L1;MAD1L1

DMRs

chr start end p length fdr sidak nprobe
16 73100425 73100790 0e+00 365 0e+00 0.0000000 3
3 148804271 148804556 0e+00 285 0e+00 0.0000004 8
3 67704889 67705285 0e+00 396 0e+00 0.0000005 6
6 161561030 161561121 0e+00 91 0e+00 0.0000071 3
7 3019158 3019382 0e+00 224 0e+00 0.0000054 4
7 27170716 27171051 0e+00 335 0e+00 0.0000047 9
13 97646638 97646765 5e-07 127 5e-07 0.0016533 4
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mn_F/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mn_F/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mn_F/Mn_log2_manhattan_DMP_adj.png")

Mn, male

DMP_Mn_M_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_M, var = 'Mn_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mn_M')

# Unadjusted, N =  192 
# Unadjusted, p<0.05:  9543 
# Unadjusted, FDR<0.05:  2 
# Unadjusted, pBonf<0.05:  2 
 
# Adjusted, N =  192 
# Adjusted, p<0.05:  12799 
# Adjusted, FDR<0.05:  2 
# Adjusted, pBonf<0.05:  2 
# Adjusted, lambda:  0.8388281 
 
# Number of DMRs identified:   4

GO_Mn_M = gometh(sig.cpg = DMP_Mn_M_cord[[3]]$cpg[DMP_Mn_M_cord[[3]]$adj.P.Val < 0.05], all.cpg = DMP_Mn_M_cord[[3]]$cpg, collection = "GO")
table(GO_Mn_M$P.DE < 0.05)
# FALSE  TRUE 
# 22586    24 
table(GO_Mn_M$FDR < 0.05)
# FALSE 
# 22610 

KEGG_Mn_M = gometh(sig.cpg = DMP_Mn_M_cord[[3]]$cpg[DMP_Mn_M_cord[[3]]$adj.P.Val < 0.05], all.cpg = DMP_Mn_M_cord[[3]]$cpg, collection = "KEGG")
table(KEGG_Mn_M$P.DE < 0.05)
# FALSE 
  # 342 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_M)
y = pDatcordMetal_M$Mn_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_M)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.3561523

TestCDFs2(Z = Z, y = y, X = X)
# 0.5219932

# rm(DMP_Mn_M_cord); gc()

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg02042823 0.51 (0.36 ,0.66) 5.71 0 0.0001241 0.0001 chr16 6714429 A2BP1;A2BP1
cg03763518 -0.29 (-0.39 ,-0.19) -3.51 0 0.0091811 0.0184 chr1 150245044 C1orf54

DMRs

chr start end p length fdr sidak nprobe
20 36148603 36149271 0e+00 668 0e+00 0.0000000 31
7 1250087 1250273 0e+00 186 0e+00 0.0000000 7
15 99789621 99789855 0e+00 234 0e+00 0.0000030 5
1 75198817 75199117 1e-07 300 1e-07 0.0001093 6
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mn_M/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mn_M/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Mn_M/Mn_log2_manhattan_DMP_adj.png")

Pb

DMP_Pb_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal, var = 'Pb_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Pb')

# Unadjusted, N =  361 
# Unadjusted, p<0.05:  25856 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  361 
# Adjusted, p<0.05:  14691 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8763417 
 
# Number of identified DMR:  0

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals)
y = pDatcordMetal$Pb_log2
X = model.matrix(~ female_d + race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.2242514

TestCDFs2(Z = Z, y = y, X = X)
# 0.9723614

# rm(DMP_Pb_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
NA NA NA NA NA NA NA NA
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Pb/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Pb/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Pb/Pb_log2_manhattan_DMP_adj.png")

Pb, female

DMP_Pb_F_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_F, var = 'Pb_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Pb_F')

# Unadjusted, N =  169 
# Unadjusted, p<0.05:  16597 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  169 
# Adjusted, p<0.05:  20414 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.132739 
 
# Number of identified DMR:  0

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_F)
y = pDatcordMetal_F$Pb_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_F)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.07160096

TestCDFs2(Z = Z, y = y, X = X)
# 0.2744584

# rm(DMP_Pb_F_cord); gc()
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Pb_F/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Pb_F/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Pb_F/Pb_log2_manhattan_DMP_adj.png")

Pb, male

DMP_Pb_M_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_M, var = 'Pb_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Pb_M')

# Unadjusted, N =  192 
# Unadjusted, p<0.05:  19998 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  192 
# Adjusted, p<0.05:  13522 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8591965 
 
# Number of DMRs identified:   2

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_M)
y = pDatcordMetal_M$Pb_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_M)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 1

TestCDFs2(Z = Z, y = y, X = X)
# 0.9140094 

# rm(DMP_Pb_M_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
14 100203941 100204258 0 317 0 1.9e-06 6
3 122640777 122641144 0 367 0 6.5e-06 4
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Pb_M/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Pb_M/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Pb_M/Pb_log2_manhattan_DMP_adj.png")

Se

DMP_Se_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal, var = 'Se_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Se')

# Unadjusted, N =  361 
# Unadjusted, p<0.05:  23447 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  361 
# Adjusted, p<0.05:  15897 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8643957 

# Number of DMRs identified:   2 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals)
y = pDatcordMetal$Se_log2
X = model.matrix(~ female_d + race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.1214307

TestCDFs2(Z = Z, y = y, X = X)
# 0.2808225

# rm(DMP_Se_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
8 144635259 144635610 0 351 0 7.90e-06 9
4 74847645 74847829 0 184 0 4.18e-05 7
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Se/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Se/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Se/Se_log2_manhattan_DMP_adj.png")

Se, female

DMP_Se_F_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_F, var = 'Se_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Se_F')

# # Unadjusted, N =  169 
# Unadjusted, p<0.05:  11702 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  169 
# Adjusted, p<0.05:  10751 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.717438 
 
# Number of DMRs identified:   4 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_F)
y = pDatcordMetal_F$Se_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_F)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.6522482

TestCDFs2(Z = Z, y = y, X = X)
# 0.876843

# rm(DMP_Se_F_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
8 144635259 144636113 0.0000000 854 0.0000000 0.0000000 12
15 75019069 75019376 0.0000000 307 0.0000000 0.0000318 10
19 1510493 1510692 0.0000000 199 0.0000000 0.0000645 4
18 23713837 23714009 0.0002329 172 0.0002329 0.4138549 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Se_F/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Se_F/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Se_F/Se_log2_manhattan_DMP_adj.png")

Se, male

DMP_Se_M_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_M, var = 'Se_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Se_M')

# Unadjusted, N =  192 
# Unadjusted, p<0.05:  28127 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  192 
# Adjusted, p<0.05:  23097 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.035939 
 
# Number of DMRs identified:   1 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_M)
y = pDatcordMetal_M$Se_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_M)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.04829198

TestCDFs2(Z = Z, y = y, X = X)
# 0.1484135 

# rm(DMP_Se_M_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
19 57742254 57742423 0 169 0 2.7e-06 6
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Se_M/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Se_M/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Se_M/Se_log2_manhattan_DMP_adj.png")

Zn

DMP_Zn_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal, var = 'Zn_log2', covar = c('female_d', 'race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Zn')

# Unadjusted, N =  361 
# Unadjusted, p<0.05:  25089 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  361 
# Adjusted, p<0.05:  37705 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.490786 
 
# Number of DMRs identified:   6 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals)
y = pDatcordMetal$Zn_log2
X = model.matrix(~ female_d + race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.6606383

TestCDFs2(Z = Z, y = y, X = X)
# 0.2234394

# rm(DMP_Zn); gc()

DMRs

chr start end p length fdr sidak nprobe
3 48632483 48632783 0.00e+00 300 0.00e+00 0.0000004 8
17 79503641 79503877 0.00e+00 236 0.00e+00 0.0000010 4
12 1973871 1974168 0.00e+00 297 0.00e+00 0.0000053 3
11 92702372 92702912 0.00e+00 540 0.00e+00 0.0000053 8
20 25129506 25129562 5.00e-06 56 6.00e-06 0.0348380 5
6 32165175 32165200 7.09e-05 25 7.09e-05 0.6735463 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Zn/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Zn/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Zn/Zn_log2_manhattan_DMP_adj.png")

Zn, female

DMP_Zn_F_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_F, var = 'Zn_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Zn_F')

# Unadjusted, N =  169 
# Unadjusted, p<0.05:  35062 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  169 
# Adjusted, p<0.05:  17286 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.062488 
 
# Number of DMRs identified:   1 

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_F)
y = pDatcordMetal_F$Zn_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_F)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.5894776

TestCDFs2(Z = Z, y = y, X = X)
# 0.2311608

# rm(DMP_Zn_F_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
3 138763669 138763910 0 241 0 0 5
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Zn_F/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Zn_F/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Zn_F/Zn_log2_manhattan_DMP_adj.png")

Zn, male

DMP_Zn_M_cord = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatcordMetal_M, var = 'Zn_log2', covar = c('race_child2', 'gestage_wks_deliv_d', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_GS_cb', 'CD4T_GS_cb', 'CD8T_GS_cb', 'Gran_GS_cb', 'Mono_GS_cb', 'NK_GS_cb', 'nRBC_GS_cb'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Zn_M')

# Unadjusted, N =  192 
# Unadjusted, p<0.05:  10405 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  192 
# Adjusted, p<0.05:  22001 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.099038 
 
# Number of DMRs identified:   4

# Global DNAm
Z = as.matrix(ComBat.Betas.Metals_M)
y = pDatcordMetal_M$Zn_log2
X = model.matrix(~ race_child2 + gestage_wks_deliv_d + age_mom_enroll_d + bmi_mom_prepreg_d + coll_grad + nullip + gt70k + smk_preg + Bcell_GS_cb + CD4T_GS_cb + CD8T_GS_cb + Gran_GS_cb + Mono_GS_cb + NK_GS_cb + nRBC_GS_cb, data = pDatcordMetal_M)[,-1]

TestDensities2(Z = Z, y = y, X = X)
# 0.8342179

TestCDFs2(Z = Z, y = y, X = X)
# 0.7287762 

# rm(DMP_Zn_M_cord); gc()

DMRs

chr start end p length fdr sidak nprobe
13 110319561 110319607 0.0000000 46 0.0000000 4.29e-05 3
5 112824496 112824765 0.0000000 269 0.0000000 9.90e-06 6
1 1361654 1361729 0.0000000 75 0.0000000 4.20e-05 3
6 31651019 31651029 0.0077377 10 0.0077377 1.00e+00 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Zn_M/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Zn_M/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/CordBlood/Zn_M/Zn_log2_manhattan_DMP_adj.png")